Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis

Bacillus cereus is an opportunistic pathogen causing food poisoning manifested by diarrhoeal or emetic syndromes. It is closely related to the animal and human pathogen Bacillus anthracis and the insect pathogen Bacillus thuringiensis, the former being used as a biological weapon and the latter as a pesticide. B. anthracis and B. thuringiensis are readily distinguished from B. cereus by the presence of plasmid-borne specific toxins (B. anthracis and B. thuringiensis) and capsule (B. anthracis). But phylogenetic studies based on the analysis of chromosomal genes bring controversial results, and it is unclear whether B. cereus, B. anthracis and B. thuringiensis are varieties of the same species or different species. Here we report the sequencing and analysis of the type strain B. cereus ATCC 14579. The complete genome sequence of B. cereus ATCC 14579 together with the gapped genome of B. anthracis A2012 enables us to perform comparative analysis, and hence to identify the genes that are conserved between B. cereus and B. anthracis, and the genes that are unique for each species. We use the former to clarify the phylogeny of the cereus group, and the latter to determine plasmid-independent species-specific markers.     

Impairment of dendritic cells and adaptive immunity by anthrax lethal toxin

Anthrax poses a clear and present danger as an agent of biological terrorism. Infection with Bacillus anthracis, the causative agent of anthrax, if untreated can result in rampant bacteraemia, multisystem dysfunction and death. Anthrax lethal toxin (LT) is a critical virulence factor of B. anthracis, which occurs as a complex of protective antigen and lethal factor. Here we demonstrate that LT severely impairs the function of dendritic cells--which are pivotal to the establishment of immunity against pathogens--and host immune responses by disrupting the mitogen-activated protein (MAP) kinase intracellular signalling network. Dendritic cells exposed to LT and then stimulated with lipopolysaccharide do not upregulate co-stimulatory molecules, secrete greatly diminished amounts of proinflammatory cytokines, and do not effectively stimulate antigen-specific T cells in vivo. Furthermore, injections of LT induce a profound impairment of antigen-specific T- and B-cell immunity. These data suggest a role for LT in suppressing host immunity during B. anthracis infections, and represent an immune evasion strategy, where a microbe targets MAP kinases in dendritic cells to disarm the immune response.     

苏芸金芽孢杆菌与蜡状芽孢杆菌基因组DNA同源性及多态性的研究

用ＲＡＰＤ－ＰＣＲ扩增到６１个标准株、生产用菌株及２４个蜡状芽孢杆菌参比菌株的全ＤＮＡ指纹图,通过计算多态性扩增片段的大小,利用ＮＴＳＹＳ软件进行聚类分析,蜡状芽孢杆菌菌株并未形成独立于苏芸金芽孢杆菌的聚群,这是此近缘种ＤＮＡ分子水平高度同源的新证据．６１个苏芸金芽孢杆菌的聚类结果表明：其ＤＮＡ指纹图与Ｈ－血清型有一定相关性．与引物０９５５－０３相比,引物０９４０－１２对苏芸金芽孢杆菌不同亚种及蜡状芽孢杆菌菌株具有更高的鉴别价值,大多数特异株ＤＮＡ全指纹图有菌株特异性,证实ＲＡＰＤ－ＰＣＲ技术是苏芸金芽孢杆菌及蜡状芽孢杆菌种下分类和鉴定的简便快速有效的方法     

Anthrax toxins cooperatively inhibit endocytic recycling by the Rab11/Sec15 exocyst

Bacillus anthracis is the causative agent of anthrax in humans and other mammals. In lethal systemic anthrax, proliferating bacilli secrete large quantities of the toxins lethal factor (LF) and oedema factor (EF), leading to widespread vascular leakage and shock. Whereas host targets of LF (mitogen-activated protein-kinase kinases) and EF (cAMP-dependent processes) have been implicated in the initial phase of anthrax, less is understood about toxin action during the final stage of infection. Here we use Drosophila melanogaster to identify the Rab11/Sec15 exocyst, which acts at the last step of endocytic recycling, as a novel target of both EF and LF. EF reduces levels of apically localized Rab11 and indirectly blocks vesicle formation by its binding partner and effector Sec15 (Sec15-GFP), whereas LF acts more directly to reduce Sec15-GFP vesicles. Convergent effects of EF and LF on Rab11/Sec15 inhibit expression of and signalling by the Notch ligand Delta and reduce DE-cadherin levels at adherens junctions. In human endothelial cells, the two toxins act in a conserved fashion to block formation of Sec15 vesicles, inhibit Notch signalling, and reduce cadherin expression at adherens junctions. This coordinated disruption of the Rab11/Sec15 exocyst by anthrax toxins may contribute to toxin-dependent barrier disruption and vascular dysfunction during B. anthracis infection.     

Anthrax kills wild chimpanzees in a tropical rainforest

Infectious disease has joined habitat loss and hunting as threats to the survival of the remaining wild populations of great apes. Nevertheless, relatively little is known about the causative agents. We investigated an unusually high number of sudden deaths observed over nine months in three communities of wild chimpanzees (Pan troglodytes verus) in the Ta? National Park, Ivory Coast. Here we report combined pathological, cytological and molecular investigations that identified Bacillus anthracis as the cause of death for at least six individuals. We show that anthrax can be found in wild non-human primates living in a tropical rainforest, a habitat not previously known to harbour B. anthracis. Anthrax is an acute disease that infects ruminants, but other mammals, including humans, can be infected through contacting or inhaling high doses of spores or by consuming meat from infected animals. Respiratory and gastrointestinal anthrax are characterized by rapid onset, fever, septicaemia and a high fatality rate without early antibiotic treatment. Our results suggest that epidemic diseases represent substantial threats to wild ape populations, and through bushmeat consumption also pose a hazard to human health.     

Screening inhibitors of anthrax lethal factor

The disease anthrax is caused by lethal factor, an enzyme component of the toxin produced by the spore-forming bacterium Bacillus anthracis. Here we describe substrate molecules for this factor that offer a means for high-throughput screening of potential inhibitors for use in anthrax treatment. Our assay should help to answer the urgent call for new and specific therapies to combat this pathogen after its recent emergence as a terrorist bioweapon.     

利用PCR-DGGE技术分析微生态制剂在传代过程中的菌群变化

利用变性梯度凝胶电泳（denaturing gradient gel electrophoresis, DGGE）技术,结合传统平板培养法对实验室研制的1种由乳酸菌和芽孢杆菌组成的微生态菌剂WS-401及其在连续转接培养过程中细菌种群组成的动态变化进行分析。WS-401原液的活菌数为2×107 cfu/mL,且细胞个体形态多样。将分离自原液的3株细菌进行DGGE分析,出现2种指纹谱带,对照标准的DGGE指纹图谱库和序列分析,分别被鉴定为蜡状芽孢杆菌（Bacillus cereus）和嗜热链球菌（Streptococcus thermophilus）。将该菌剂分别在LB和MRS两种培养基中30℃或37℃连续转接5次,DGGE分析每次转接后培养物的菌群组成,结果发现,随着转接次数的增加,微生物菌群的种类减少,在LB培养基中转接5次后优势菌群只有蜡状芽胞杆菌,而在MRS培养基中转接后优势菌群为植物乳杆菌（Lactobacillus plantarum）和类干酪乳杆菌（Lactobacillus paracasei）。由此说明,微生物的营养基质和培养条件对微生态制剂在传代过程中的菌群组成和动态变化有重要影响。     

病原芽胞杆菌几丁质酶产生菌的筛选与活性鉴定

通过特异引物PCR方法和水解圈活性法对62株苏云金芽胞杆菌菌株、26株蜡状芽胞杆菌菌株及18株球形芽胞杆菌菌株进行了几丁质酶产生菌的筛选.所测苏云金芽胞杆菌中除4株野生型菌株外均为阳性结果,蜡状芽胞杆菌仅1株为阴性结果,球形芽胞杆菌全为阴性结果,且水解圈法观察结果与PCR检测结果一致.在此基础上,通过DNS比色法对几丁质酶产生菌株的几丁质酶比活力也进行了测定.对这些具有致病性的病原芽胞杆菌几丁质酶的研究对于研究其致病机理及对其进行遗传改良具有重要的理论和实际应用价值.     

蜡质芽孢杆菌酰基高丝氨酸内酯酶基因的克隆及序列分析

利用pMD18-T克隆载体从蜡质芽孢杆菌菌株T—HW3中克隆了酰基高丝氨酸内酯酶基因（AHL—lactonase，aiiA）。测序结果表明，该基因（GenBank登录号为DQ000643）由753个碱基组成，编码含有250个氨基酸残基的蛋白质。该蛋白质的推测的分子量为28kDa，等电点为4．235左右。核苷酸序列的BLAST分析结果表明，与之同源性较高的基因均为蜡质芽孢杆菌组aiiA基因（86％-99％）。     

饲料中蜡状芽孢杆菌的分离与鉴定

从西宁市某饲料厂随机采集饲料样品70份,进行蜡状芽孢杆菌的常规分离培养与鉴定。共检出阳性菌株31株,检出率44．29％（31／70）,31株分离株的生化试验结果与蜡状芽孢杆菌完全一致,且31株分离株都具有营养要求低、生长速度快的特点。     

The protein kinase PKR is required for macrophage apoptosis after activation of Toll-like receptor 4

Macrophages are pivotal constituents of the innate immune system, vital for recognition and elimination of microbial pathogens. Macrophages use Toll-like receptors (TLRs) to detect pathogen-associated molecular patterns--including bacterial cell wall components, such as lipopolysaccharide or lipoteichoic acid, and viral nucleic acids, such as double-stranded (ds)RNA--and in turn activate effector functions, including anti-apoptotic signalling pathways. Certain pathogens, however, such as Salmonella spp., Shigellae spp. and Yersiniae spp., use specialized virulence factors to overcome these protective responses and induce macrophage apoptosis. We found that the anthrax bacterium, Bacillus anthracis, selectively induces apoptosis of activated macrophages through its lethal toxin, which prevents activation of the anti-apoptotic p38 mitogen-activated protein kinase. We now demonstrate that macrophage apoptosis by three different bacterial pathogens depends on activation of TLR4. Dissection of anti- and pro-apoptotic signalling events triggered by TLR4 identified the dsRNA responsive protein kinase PKR as a critical mediator of pathogen-induced macrophage apoptosis. The pro-apoptotic actions of PKR are mediated both through inhibition of protein synthesis and activation of interferon response factor 3.     

泡桐内生枯草芽孢杆菌JDB-1草菌素的抑菌活性及其spaS基因的克隆

用硫酸铵沉淀法从泡桐内生枯草芽孢杆菌JDB-1发酵液中粗提枯草菌素,采用纸片扩散法和琼脂糖扩散法分别检测枯草菌素对细菌和真菌的抑菌活性,采用PCR从菌株JDB-1基因组DNA中扩增出枯草菌素基因spaS,并克隆到pMD18-T载体,测定spaS基因的核苷酸序列.结果表明硫酸铵粗提的枯草菌素对大肠杆菌K12、恶臭假单胞杆...     

The Caenorhabditis elegans lin-12 gene encodes a transmembrane protein with overall similarity to Drosophila Notch

The lin-12 gene seems to control certain binary decisions during Caenorhabditis elegans development, from genetic and anatomical studies of lin-12 mutants that have either elevated or reduced levels of lin-12 activity. We report here the complete DNA sequence of lin-12: 13.5 kilobases (kb) derived from genomic clones and 4.5 kb from complementary DNA clones. It is of interest that the predicted product is a putative transmembrane protein, given that many of the decisions controlled by lin-12 activity require cell-cell interactions for the correct choice of cell fate. In addition, the predicted lin-12 product may be classified into several regions, based on amino acid sequence similarities to other proteins. These include extensive overall sequence similarity to the Drosophila Notch protein, which also is involved in cell-cell interactions that specify cell fate; a repeated motif found in proteins encoded by the yeast cell-cycle control genes cdc10 (Schizosaccharomyces pombe) and SWI6 (Saccharomyces cerevisiae); and a repeated motif exemplified by epidermal growth factor, found in many mammalian proteins.     

The complete DNA sequence of yeast chromosome III.

The entire DNA sequence of chromosome III of the yeast Saccharomyces cerevisiae has been determined. This is the first complete sequence analysis of an entire chromosome from any organism. The 315-kilobase sequence reveals 182 open reading frames for proteins longer than 100 amino acids, of which 37 correspond to known genes and 29 more show some similarity to sequences in databases. Of 55 new open reading frames analysed by gene disruption, three are essential genes; of 42 non-essential genes that were tested, 14 show some discernible effect on phenotype and the remaining 28 have no overt function.     

Unusual sequences in the murine immunoglobulin mu-delta heavy-chain region

The delta heavy (H) chain of mouse immunoglobulin D (IgD) is unusual both in its structure and in its differential expression relative to immunoglobulin M (IgM; reviewed in ref. 1). The region of DNA between IgM and IgD H-chain constant-region genes is probably implicated in this control. So far only fragments of the area have been sequenced. Now, however, we present the complete sequence as well as the sequence of the introns of the C delta gene. We have found several interesting features (Fig. 1), including an open reading frame (ORF) between Cmu and C delta which encodes 146 amino acids that might represent a previously unsuspected domain-like protein; three blocks of simple repetitive sequences; a 162-base pair (bp) unique-sequence inverted repeat; and a domain-like pseudogene in the large intron of C delta. We have not found, however, any sequence 5' of C delta resembling the switch (S) recombination sequences associated with class switching in other heavy chains. Moreover, we have determined the 3' deletion end point of an IgD-producing myeloma and find no sequences reminiscent of switch sites nearby.     

The proteins of linked genes evolve at similar rates

Much more variation in the rate of protein evolution occurs than is expected by chance. But why some proteins evolve rapidly but others slowly is poorly resolved. It was proposed, for example, that essential genes might evolve slower than dispensable ones, but this is not the case; and despite earlier claims, rates of evolution do not correlate with amino-acid composition. A few patterns have been found: proteins involved in antagonistic co-evolution (for example, immune genes, parasite antigens and reproductive conflict genes) tend to be rapidly evolving, and there is a correlation between the rate of protein evolution and the mutation rate of the gene. Here we report a new highly statistically significant predictor of a protein's rate of evolution, and show that linked genes have similar rates of protein evolution. There is also a weaker similarity of rates of silent site evolution (see ref. 13), which appears to be, in part, a consequence of the similarity in rates of protein evolution. The similarity in rates of protein evolution is not a consequence of underlying mutational patterns. A pronounced negative correlation between the rate of protein evolution and a covariant of the recombination rate indicates that rates of protein evolution possibly reflect, in part, the local strength of stabilizing selection.     

纤维素降解菌的分离及单菌株与菌群纤维素酶活性质

从实验室保存的5号菌群中，分离筛选出四株具有纤维素酶活力的细菌F1、F2、F3和F4．经形态学观察并进行16SrDNA序列分析，鉴定F1、F2、F3、F4分别是苏云金芽孢杆菌、生淀粉糖化酶产生菌、粪产碱菌和蜡样芽孢杆菌．通过分别测定四株细菌、5号菌群以及四株菌混合菌群的CMC酶活．进行比较分析，说明分离筛选单菌株，了解了菌群主要成分，同时有利于克服5号菌群活性不稳定，无法保存等缺点．混合单菌株形成新的菌群，利于后续对菌群内部各组分之间相互作用的研究．     

Evolutionary origin of a calcium-dependent protease by fusion of genes for a thiol protease and a calcium-binding protein?

Calcium-dependent protease (calcium protease) is apparently involved in a variety of cellular processes. Here we have attempted to clarify the role and regulatory mechanism of calcium protease by analysing its structure. The complete primary structure of calcium protease (relative molecular mass (Mr) 80,000 (80K), 705 amino acids) was deduced from the nucleotide sequence of cloned complementary DNA. The protein contains four distinct domains, and we have observed a marked similarity between the second and fourth domains and the papain-like thiol proteases and calmodulin-like calcium-binding proteins, respectively. This finding suggests that calcium protease arose from the fusion of genes for proteins of completely different function and evolutionary origin. Further, it provides functional insight into cellular regulatory mechanisms mediated by Ca2+ through calcium-binding proteins.     

The Pas2 protein essential for peroxisome biogenesis is related to ubiquitin-conjugating enzymes.

In the yeast Saccharomyces cerevisiae, PAS genes are essential for the biogenesis and proliferation of peroxisomes. Recently, the first two genes, PAS1 (ref. 3) and PAS3 (ref. 4), have been characterized. Here we report the cloning and sequencing of the PAS2 gene. It encodes a new member of the ubiquitin-conjugating (UBC) protein family and is the first member associated with peroxisomes. The proposed function of the Pas2 protein as a UBC enzyme (UBC10) is supported by the fact that site-directed mutagenesis of a strictly conserved and functionally essential cysteine residue of UBC proteins leads to mutant Pas2 proteins unable to complement pas2 mutant strains. Ubiquitination of proteins is known to play an important part in DNA repair, sporulation, cell cycle control and degradation of abnormal proteins. We provide evidence for a crucial role of the ubiquitin-conjugation pathway in organelle formation.